A bioinformatics tool for working with modified bases
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
bam{:bash}
:file
Sorted BAM/CRAM file
*.{bam,cram}
bai{:bash}
Associated index file for BAM
*.bai
meta2{:bash}
Groovy Map containing reference information e.g. [ id:'hg38' ]
[ id:'hg38' ]
fasta{:bash}
Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering
*.fasta
fai{:bash}
Associated index file for FASTA
*.fai
meta3{:bash}
Groovy Map containing BED file information e.g. [ id:'regions' ]
[ id:'regions' ]
bed{:bash}
BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the file
*.bed
*.bed{:bash}
bedMethyl output file(s)
bedgraph{:bash}
*.bedgraph{:bash}
bedgraph output files
*.bedgraph
log{:bash}
*.log{:bash}
File for debug logs to be written to
*.log
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data
